1,342 results on '"Vivek, B."'
Search Results
2. Organ Donation after Circulatory Determination of Death - Consensus Statement
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Avnish Kumar Seth, Ravi Mohanka, Raj Kumar Mani, Sonal Asthana, Sandeep Attawar, Kumud K. Dhital, Deepak Gupta, Roop Gursahani, Milind Hote, Anil Kumar, Krishan Kumar, Vivek B. Kute, Surendra Kumar Mathur, Dhvani Mehta, Darius F. Mirza, Pranjal Modi, Rahul Anil Pandit, Ashish Sharma, and Sunil Shroff
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advance medical directives ,circulatory determination of death ,controlled determination of death by circulatory criteria ,delinking organ donation ,determining futility of care ,donation after circulatory death ,do-not attempt resuscitation ,end-of-life care ,ex vivo machine perfusion ,life-sustaining treatments ,maastricht classification ,machine perfusion ,normothermic perfusion ,no-touch period ,organ preservation ,retrieval in controlled determination of death by circulatory criteria ,supreme court judgement ,surrogate decision maker ,uncontrolled determination of death by circulatory criteria ,withdrawal of care ,withdrawal of life-sustaining treatment ,Surgery ,RD1-811 - Abstract
Organ donation after circulatory determination of death (DCDD) has contributed significantly to the donor pool in several countries, most commonly being category III-controlled donations. This document, prepared by a multidisciplinary group of experts, describes the feasibility of category III DCDD in India, in view of the January 2023 Supreme Court (SC) judgment simplifying the process of withdrawal of life-sustaining treatment (WLST). The paper discusses the concept and types of futility of care, how to elicit patients values and wishes, outlines its determination in several clinical situations and the process of WLST in such cases, in accordance with the SC judgement. The judgement mandates evaluation for futility of care by the primary and secondary medical boards before intimation to the judicial magistrate and WLST. The paper also discusses the use of new and upcoming organ preservation techniques and technologies in various organ transplants and outcomes of such transplants. We have also reviewed international best practices in cDCDD, discuss the ethical, medical, legal, economic, procedural, and logistic challenges in India and outline a path for DCDD in India. The manuscript discusses and compares the timing and location of WLST, consent for antemortem measures, no-touch period, and the possibility of stand-down and return to the intensive care unit (ICU) without donation. Further clarifications of aspects such as ante-mortem measures and do-not attempt resuscitation (DNAR) may be required during implementation of the judgement in some situations.
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- 2024
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3. Vimentin is a key regulator of cell mechanosensing through opposite actions on actomyosin and microtubule networks
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Alisafaei, Farid, Mandal, Kalpana, Saldanha, Renita, Swoger, Maxx, Yang, Haiqian, Shi, Xuechen, Guo, Ming, Hehnly, Heidi, Castañeda, Carlos A., Janmey, Paul A., Patteson, Alison E., and Shenoy, Vivek B.
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- 2024
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4. Active transcription and epigenetic reactions synergistically regulate meso-scale genomic organization
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Kant, Aayush, Guo, Zixian, Vinayak, Vinayak, Neguembor, Maria Victoria, Li, Wing Shun, Agrawal, Vasundhara, Pujadas, Emily, Almassalha, Luay, Backman, Vadim, Lakadamyali, Melike, Cosma, Maria Pia, and Shenoy, Vivek B.
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- 2024
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5. Vimentin is a key regulator of cell mechanosensing through opposite actions on actomyosin and microtubule networks
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Farid Alisafaei, Kalpana Mandal, Renita Saldanha, Maxx Swoger, Haiqian Yang, Xuechen Shi, Ming Guo, Heidi Hehnly, Carlos A. Castañeda, Paul A. Janmey, Alison E. Patteson, and Vivek B. Shenoy
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Biology (General) ,QH301-705.5 - Abstract
Abstract The cytoskeleton is a complex network of interconnected biopolymers consisting of actin filaments, microtubules, and intermediate filaments. These biopolymers work in concert to transmit cell-generated forces to the extracellular matrix required for cell motility, wound healing, and tissue maintenance. While we know cell-generated forces are driven by actomyosin contractility and balanced by microtubule network resistance, the effect of intermediate filaments on cellular forces is unclear. Using a combination of theoretical modeling and experiments, we show that vimentin intermediate filaments tune cell stress by assisting in both actomyosin-based force transmission and reinforcement of microtubule networks under compression. We show that the competition between these two opposing effects of vimentin is regulated by the microenvironment stiffness. These results reconcile seemingly contradictory results in the literature and provide a unified description of vimentin’s effects on the transmission of cell contractile forces to the extracellular matrix.
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- 2024
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6. Active transcription and epigenetic reactions synergistically regulate meso-scale genomic organization
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Aayush Kant, Zixian Guo, Vinayak Vinayak, Maria Victoria Neguembor, Wing Shun Li, Vasundhara Agrawal, Emily Pujadas, Luay Almassalha, Vadim Backman, Melike Lakadamyali, Maria Pia Cosma, and Vivek B. Shenoy
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Science - Abstract
Abstract In interphase nuclei, chromatin forms dense domains of characteristic sizes, but the influence of transcription and histone modifications on domain size is not understood. We present a theoretical model exploring this relationship, considering chromatin-chromatin interactions, histone modifications, and chromatin extrusion. We predict that the size of heterochromatic domains is governed by a balance among the diffusive flux of methylated histones sustaining them and the acetylation reactions in the domains and the process of loop extrusion via supercoiling by RNAPII at their periphery, which contributes to size reduction. Super-resolution and nano-imaging of five distinct cell lines confirm the predictions indicating that the absence of transcription leads to larger heterochromatin domains. Furthermore, the model accurately reproduces the findings regarding how transcription-mediated supercoiling loss can mitigate the impacts of excessive cohesin loading. Our findings shed light on the role of transcription in genome organization, offering insights into chromatin dynamics and potential therapeutic targets.
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- 2024
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7. Review: Perovskite nanostructures materials versatile platform for advance biosensor applications
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Vivek B. Korde, Suhas Khot, Dinkar B. Kamble, and Shankar Amalraj
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Nanobiosensor ,Biosensing ,Biomolecules ,Perovskite ,Instruments and machines ,QA71-90 - Abstract
The distinct presence of a central atom surrounded by eight ligands leads to higher light absorption and charge carrier mobility in perovskite materials. The peculiar nature of the structure inspires all the scientists and researchers to work more in sustainable applications, such as solar cells, light emitting diodes, transistor and biosensors. The capability of perovskite material in detecting smaller molecules such as O2, NO2 and CO2 is higher. Therefore, several biosensors are demonstrated based on the perovskite nanomaterial to various chemical and biological species with both solid and solution states. The immense sources of research articles thrived the author, to review the perovskite nanomaterials in the dimension of biosensor application extensively. This review covers major three areas of perovskite nanomaterial, such as components and characteristics of biosensors, properties and preparation of perovskite materials and application and research trends of perovskite nanostructure biosensor.
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- 2024
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8. De novo Donor-specific Anti-human Leukocyte Antigen Antibody and Its Outcome in Pediatric Renal Transplant Recipients: A Single-center Experience in India
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Anshuman Saha, Shahenaz F. Kapadia, Kinnari B. Vala, Varsha B Trivedi, Himanshu V Patel, Pankaj R. Shah, and Vivek B. Kute
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Medicine - Abstract
Development of de novo donor-specific anti-HLA antibody (dnDSA) is associated with poor graft survival in adults. However, there is a paucity of data about its prevalence and outcome in Indian children. We retrospectively assessed the proportion and spectrum of dnDSA and its outcome on antibody-mediated rejection (ABMR) and graft function. Children ≤18 years who were transplanted between November 2016 and October 2019 were included in this study. Pretransplant donor-specific antibody (DSA) was screened by complement-dependent cytotoxicity, flow cytometry crossmatch, and single antigen bead (SAB) class I and II by Luminex platform. Either antithymocyte globulin or basiliximab was used as induction. Tacrolimus, mycophenolate, and prednisolone were used for the maintenance of immunosuppression. SAB screening was done at 1, 3, 6 months, and yearly in seven children and at the time of acute graft dysfunction in eight. Mean fluorescence intensity ≥1000 was considered positive. Protocol biopsies were done at 3, 6, and 12 months and annually thereafter in seven children. Fifteen children, all males with a median age (interquartile range) of 13 years (11; 15.5) were analyzed. Only one child had pretransplant DSA who developed dnDSA posttransplant. Overall, 8 (53%) developed dnDSA over a median follow-up of 18 months. Seven (87%) had Class II, one Class I and 3 (37%) both Class I and II. Six had dQ and two had DR. All children with dnDSA had ABMR, of these two had subclinical rejection. DSAs persisted despite treatment, though graft function improved. Children with DSA and ABMR had lower graft function than those without DSA. The proportion of dnDSA was high in our study, majority against DQ. The detection of dnDSA prompted early diagnosis and treatment of ABMR.
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- 2023
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9. The separation pin distinguishes the pro– and anti–recombinogenic functions of Saccharomyces cerevisiae Srs2
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Aviv Meir, Vivek B. Raina, Carly E. Rivera, Léa Marie, Lorraine S. Symington, and Eric C. Greene
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Science - Abstract
Abstract Srs2 is an Sf1a helicase that helps maintain genome stability in Saccharomyces cerevisiae through its ability to regulate homologous recombination. Srs2 downregulates HR by stripping Rad51 from single–stranded DNA, and Srs2 is also thought to promote synthesis–dependent strand annealing by unwinding D–loops. However, it has not been possible to evaluate the relative contributions of these two distinct activities to any aspect of recombination. Here, we used a structure–based approach to design an Srs2 separation–of–function mutant that can dismantle Rad51–ssDNA filaments but is incapable of disrupting D–loops, allowing us to assess the relative contributions of these pro– and anti–recombinogenic functions. We show that this separation–of–function mutant phenocopies wild–type SRS2 in vivo, suggesting that the ability of Srs2 to remove Rad51 from ssDNA is its primary role during HR.
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- 2023
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10. Review: Perovskite nanostructures materials versatile platform for advance biosensor applications
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Korde, Vivek B., Khot, Suhas, Kamble, Dinkar B., and Amalraj, Shankar
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- 2024
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11. The separation pin distinguishes the pro– and anti–recombinogenic functions of Saccharomyces cerevisiae Srs2
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Meir, Aviv, Raina, Vivek B., Rivera, Carly E., Marie, Léa, Symington, Lorraine S., and Greene, Eric C.
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- 2023
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12. Chemo-mechanical diffusion waves explain collective dynamics of immune cell podosomes
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Gong, Ze, van den Dries, Koen, Migueles-Ramírez, Rodrigo A., Wiseman, Paul W., Cambi, Alessandra, and Shenoy, Vivek B.
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- 2023
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13. Stress-resilient maize for climate-vulnerable ecologies in the Asian tropics
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Zaidi, P H, Nguyen, Thanh, Ha, Dang N, Thaitad, Suriphat, Ahmed, Salahuddin, Arshad, Muhammad, Koirala, Keshav B, Rijal, Tirtha R, Kuchanur, Prakash H, Patil, Ayyanagouda, Mandal, Shyam S, Kumar, Ramesh, Singh, S B, Kumar, Bhupender, Shahi, J P, Patel, M B, Gumma, Murali K, Pandey, Kamal, Chaurasia, Ramesh, Haque, Azizul, Seetharam, K, Das, Reshmi R, Vinayan, M T, Rashid, Zerka, Nair, S K, and Vivek, B S
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- 2020
14. Direct Opto-Electronic Imaging of 2D Semiconductor - 3D Metal Buried Interfaces
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Jo, Kiyoung, Kumar, Pawan, Orr, Joseph, Anantharaman, Surendra B., Miao, Jinshui, Motala, Michael, Bandyopadhyay, Arkamita, Kisslinger, Kim, Muratore, Christopher, Shenoy, Vivek B., Stach, Eric, Glavin, Nicholas, and Jariwala, Deep
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Condensed Matter - Mesoscale and Nanoscale Physics ,Condensed Matter - Materials Science ,Physics - Applied Physics ,Physics - Optics - Abstract
The semiconductor-metal junction is one of the most critical factors for high performance electronic devices. In two-dimensional (2D) semiconductor devices, minimizing the voltage drop at this junction is particularly challenging and important. Despite numerous studies concerning contact resistance in 2D semiconductors, the exact nature of the buried interface under a three-dimensional (3D) metal remains unclear. Herein, we report the direct measurement of electrical and optical responses of 2D semiconductor-metal buried interfaces using a recently developed metal-assisted transfer technique to expose the buried interface which is then directly investigated using scanning probe techniques. We characterize the spatially varying electronic and optical properties of this buried interface with < 20 nm resolution. To be specific, potential, conductance and photoluminescence at the buried metal/MoS$_2$ interface are correlated as a function of a variety of metal deposition conditions as well as the type of metal contacts. We observe that direct evaporation of Au on MoS$_2$ induces a large strain of ~5% in the MoS$_2$ which, coupled with charge transfer, leads to degenerate doping of the MoS$_2$ underneath the contact. These factors lead to improvement of contact resistance to record values of 138 kohm-um, as measured using local conductance probes. This approach was adopted to characterize MoS$_2$-In/Au alloy interfaces, demonstrating contact resistance as low as 63 kohm-um. Our results highlight that the MoS$_2$/Metal interface is sensitive to device fabrication methods, and provides a universal strategy to characterize buried contact interfaces involving 2D semiconductors., Comment: 6 figures + supplement
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- 2021
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15. Incidence and risk factors for any retinopathy of prematurity (ROP) and type 1 ROP in a neonatal care unit (NICU) in North Karnataka
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Vivek B. Wani, Praneet Telukunta, Arvind L. Tenagi, Shivanand B. Patil, Bhagyajyothi B. Khanagavi, Niranjana S. Mahantshetti, Manisha Bhandankar, and Sangappa M Dhaded
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retinopathy of prematurity ,type 1 rop ,incidence ,risk factors ,treatment outcomes ,Therapeutics. Pharmacology ,RM1-950 ,Toxicology. Poisons ,RA1190-1270 - Abstract
Purpose: To report the incidence and risk factors for any ROP and type 1 ROP and treatment outcomes of type 1 ROP. Methods and Material: Infants born in our hospital with gestational age (GA) of < 34weeks or birth weight (BW) < 2000g were screened for ROP and treated if type 1 ROP developed. Incidence of any ROP and type 1 ROP were calculated. Several variables were evaluated by univariate and multivariate analyses to find their significance for any ROP and type 1 ROP. Results of treatment for type 1 ROP are reported. Results: Out of 263 infants screened, 64 (24.3%) developed any ROP and 15(5.7%) type 1 ROP. All the eyes with type 1 ROP showed complete regression after treatment. Multivariate analysis showed that; infants with GA of 31-34 weeks had significantly less any ROP (P=0.002) and type 1 ROP (p= 0.020) versus infants of GA ≤30w. Infants with BW≥1501g had less any ROP (P=0.025) and less type 1 ROP (P=0.018) versus infants with BW ≤1250g. Infants with BW 1251g to 1500g had less type 1 ROP versus infants with BW≤1250g. (P=0.042) and females had significantly less type 1 ROP (P= 0.012) versus male infants. Conclusions: The incidence of any ROP and type 1 ROP were relatively low in our study. Type 1 ROP regressed completely in all eyes after treatment. GA, BW and gender were significant factors for any ROP and type 1 ROP.
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- 2023
16. High-throughput search for magnetic and topological order in transition metal oxides
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Frey, Nathan C., Horton, Matthew K., Munro, Jason M., Griffin, Sinéad M., Persson, Kristin A., and Shenoy, Vivek B.
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Condensed Matter - Materials Science ,Condensed Matter - Strongly Correlated Electrons ,Physics - Computational Physics - Abstract
The discovery of intrinsic magnetic topological order in $\rm MnBi_2Te_4$ has invigorated the search for materials with coexisting magnetic and topological phases. These multi-order quantum materials are expected to exhibit new topological phases that can be tuned with magnetic fields, but the search for such materials is stymied by difficulties in predicting magnetic structure and stability. Here, we compute over 27,000 unique magnetic orderings for over 3,000 transition metal oxides in the Materials Project database to determine their magnetic ground states and estimate their effective exchange parameters and critical temperatures. We perform a high-throughput band topology analysis of centrosymmetric magnetic materials, calculate topological invariants, and identify 18 new candidate ferromagnetic topological semimetals, axion insulators, and antiferromagnetic topological insulators. To accelerate future efforts, machine learning classifiers are trained to predict both magnetic ground states and magnetic topological order without requiring first-principles calculations., Comment: 9 pages, 6 figures
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- 2020
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17. Single-step Adversarial training with Dropout Scheduling
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S., Vivek B. and Babu, R. Venkatesh
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Computer Science - Machine Learning ,Computer Science - Computer Vision and Pattern Recognition - Abstract
Deep learning models have shown impressive performance across a spectrum of computer vision applications including medical diagnosis and autonomous driving. One of the major concerns that these models face is their susceptibility to adversarial attacks. Realizing the importance of this issue, more researchers are working towards developing robust models that are less affected by adversarial attacks. Adversarial training method shows promising results in this direction. In adversarial training regime, models are trained with mini-batches augmented with adversarial samples. Fast and simple methods (e.g., single-step gradient ascent) are used for generating adversarial samples, in order to reduce computational complexity. It is shown that models trained using single-step adversarial training method (adversarial samples are generated using non-iterative method) are pseudo robust. Further, this pseudo robustness of models is attributed to the gradient masking effect. However, existing works fail to explain when and why gradient masking effect occurs during single-step adversarial training. In this work, (i) we show that models trained using single-step adversarial training method learn to prevent the generation of single-step adversaries, and this is due to over-fitting of the model during the initial stages of training, and (ii) to mitigate this effect, we propose a single-step adversarial training method with dropout scheduling. Unlike models trained using existing single-step adversarial training methods, models trained using the proposed single-step adversarial training method are robust against both single-step and multi-step adversarial attacks, and the performance is on par with models trained using computationally expensive multi-step adversarial training methods, in white-box and black-box settings., Comment: CVPR 2020
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- 2020
18. Towards Achieving Adversarial Robustness by Enforcing Feature Consistency Across Bit Planes
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Addepalli, Sravanti, S., Vivek B., Baburaj, Arya, Sriramanan, Gaurang, and Babu, R. Venkatesh
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Computer Science - Computer Vision and Pattern Recognition ,Computer Science - Cryptography and Security ,Computer Science - Machine Learning - Abstract
As humans, we inherently perceive images based on their predominant features, and ignore noise embedded within lower bit planes. On the contrary, Deep Neural Networks are known to confidently misclassify images corrupted with meticulously crafted perturbations that are nearly imperceptible to the human eye. In this work, we attempt to address this problem by training networks to form coarse impressions based on the information in higher bit planes, and use the lower bit planes only to refine their prediction. We demonstrate that, by imposing consistency on the representations learned across differently quantized images, the adversarial robustness of networks improves significantly when compared to a normally trained model. Present state-of-the-art defenses against adversarial attacks require the networks to be explicitly trained using adversarial samples that are computationally expensive to generate. While such methods that use adversarial training continue to achieve the best results, this work paves the way towards achieving robustness without having to explicitly train on adversarial samples. The proposed approach is therefore faster, and also closer to the natural learning process in humans., Comment: CVPR 2020
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- 2020
19. Direct Visualisation of Out-of-Equilibrium Structural Transformations in Atomically-Thin Chalcogenides
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Kumar, Pawan, Horwath, James P., Foucher, Alexandre C., Price, Christopher C., Acero, Natalia, Shenoy, Vivek B., Stach, Eric A., and Jariwala, Deep
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Condensed Matter - Materials Science ,Condensed Matter - Disordered Systems and Neural Networks ,Condensed Matter - Mesoscale and Nanoscale Physics ,Physics - Applied Physics - Abstract
Two-dimensional (2D) transition metal dichalcogenides (TMDCs) have been the subject of sustained research interest due to their extraordinary electronic and optical properties. They also exhibit a wide range of structural phases because of the different orientations that the atoms can have within a single layer, or due to the ways that different layers can stack. Here we report the first study of direct-visualization of structural transformations in atomically-thin layers under highly non-equilibrium thermodynamic conditions. We probe these transformations at the atomic scale using real-time, aberration corrected scanning transmission electron microscopy and observe strong dependence of the resulting structures and phases on both heating rate and temperature. A fast heating rate (25 C/sec) yields highly ordered crystalline hexagonal islands of sizes of less than 20 nm which are composed of a mixture of 2H and 3R phases. However, a slow heating rate (25 C/min) yields nanocrystalline and sub-stoichiometric amorphous regions. These differences are explained by different rates of sulfur evaporation and redeposition. The use of non-equilibrium heating rates to achieve highly crystalline and quantum-confined features from 2D atomic layers present a new route to synthesize atomically-thin, laterally confined nanostrucutres and opens new avenues for investigating fundamental electronic phenomena in confined dimensions.
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- 2020
20. Regularizers for Single-step Adversarial Training
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Vivek, B. S. and Babu, R. Venkatesh
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Computer Science - Machine Learning ,Computer Science - Computer Vision and Pattern Recognition - Abstract
The progress in the last decade has enabled machine learning models to achieve impressive performance across a wide range of tasks in Computer Vision. However, a plethora of works have demonstrated the susceptibility of these models to adversarial samples. Adversarial training procedure has been proposed to defend against such adversarial attacks. Adversarial training methods augment mini-batches with adversarial samples, and typically single-step (non-iterative) methods are used for generating these adversarial samples. However, models trained using single-step adversarial training converge to degenerative minima where the model merely appears to be robust. The pseudo robustness of these models is due to the gradient masking effect. Although multi-step adversarial training helps to learn robust models, they are hard to scale due to the use of iterative methods for generating adversarial samples. To address these issues, we propose three different types of regularizers that help to learn robust models using single-step adversarial training methods. The proposed regularizers mitigate the effect of gradient masking by harnessing on properties that differentiate a robust model from that of a pseudo robust model. Performance of models trained using the proposed regularizers is on par with models trained using computationally expensive multi-step adversarial training methods.
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- 2020
21. Chemo-mechanical diffusion waves explain collective dynamics of immune cell podosomes
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Ze Gong, Koen van den Dries, Rodrigo A. Migueles-Ramírez, Paul W. Wiseman, Alessandra Cambi, and Vivek B. Shenoy
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Science - Abstract
Abstract Immune cells, such as macrophages and dendritic cells, can utilize podosomes, mechanosensitive actin-rich protrusions, to generate forces, migrate, and patrol for foreign antigens. Individual podosomes probe their microenvironment through periodic protrusion and retraction cycles (height oscillations), while oscillations of multiple podosomes in a cluster are coordinated in a wave-like fashion. However, the mechanisms governing both the individual oscillations and the collective wave-like dynamics remain unclear. Here, by integrating actin polymerization, myosin contractility, actin diffusion, and mechanosensitive signaling, we develop a chemo-mechanical model for podosome dynamics in clusters. Our model reveals that podosomes show oscillatory growth when actin polymerization-driven protrusion and signaling-associated myosin contraction occur at similar rates, while the diffusion of actin monomers drives wave-like coordination of podosome oscillations. Our theoretical predictions are validated by different pharmacological treatments and the impact of microenvironment stiffness on chemo-mechanical waves. Our proposed framework can shed light on the role of podosomes in immune cell mechanosensing within the context of wound healing and cancer immunotherapy.
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- 2023
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22. High-throughput search for magnetic and topological order in transition metal oxides
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Frey, Nathan C, Horton, Matthew K, Munro, Jason M, Griffin, Sinéad M, Persson, Kristin A, and Shenoy, Vivek B
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Quantum Physics ,Physical Sciences ,Condensed Matter Physics - Abstract
The discovery of intrinsic magnetic topological order in MnBi2Te4 has invigorated the search for materials with coexisting magnetic and topological phases. These multiorder quantum materials are expected to exhibit new topological phases that can be tuned with magnetic fields, but the search for such materials is stymied by difficulties in predicting magnetic structure and stability. Here, we compute more than 27,000 unique magnetic orderings for more than 3000 transition metal oxides in the Materials Project database to determine their magnetic ground states and estimate their effective exchange parameters and critical temperatures. We perform a high-throughput band topology analysis of centrosymmetric magnetic materials, calculate topological invariants, and identify 18 new candidate ferromagnetic topological semimetals, axion insulators, and antiferromagnetic topological insulators. To accelerate future efforts, machine learning classifiers are trained to predict both magnetic ground states and magnetic topological order without requiring first-principles calculations.
- Published
- 2020
23. Modeling the vertical growth of van der Waals stacked 2D materials using the diffuse domain method
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Guo, Zhenlin, Price, Christopher, Shenoy, Vivek B., and Lowengrub, John
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Physics - Computational Physics - Abstract
Vertically-stacked monolayers of graphene and other atomically-thin 2D materials have attracted considerable research interest because of their potential in fabricating materials with specifically-designed properties. Chemical vapor deposition has proved to be an efficient and scalable fabrication method. However, a lack of mechanistic understanding has hampered efforts to control the fabrication process beyond empirical trial-and-error approaches. In this paper, we develop a general multiscale Burton-Cabrera-Frank (BCF) type model of the vertical growth of 2D materials to predict the necessary growth conditions for vertical versus in-plane (monolayer) growth of arbitrarily-shaped layers. This extends previous work where we developed such a model assuming the layers were fully-faceted (Ye et al., ACS Nano, 11, 12780-12788, 2017). To solve the model numerically, we reformulate the system using the phase-field/diffuse domain method that enables the equations to be solved in a fixed regular domain. We use a second-order accurate, adaptive finite-difference/nonlinear multigrid algorithm to discretize and solve the discrete system. We investigate the effect of parameters, including the van der Waals interaction energies between the layers, the kinetic attachment rates, the edge-energies and the deposition flux, on layer growth and morphologies. While the conditions that favor vertical growth generally follow an analytic thermodynamic criterion we derived for circular layers, the layer boundaries may develop significant curvature during growth, consistent with experimental observations. Our approach provides a mechanistic framework for controlling and optimizing the growth multilayered 2D materials.
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- 2019
24. FDA: Feature Disruptive Attack
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Ganeshan, Aditya, Vivek, B. S., and Babu, R. Venkatesh
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Computer Science - Computer Vision and Pattern Recognition ,Computer Science - Artificial Intelligence ,Computer Science - Machine Learning - Abstract
Though Deep Neural Networks (DNN) show excellent performance across various computer vision tasks, several works show their vulnerability to adversarial samples, i.e., image samples with imperceptible noise engineered to manipulate the network's prediction. Adversarial sample generation methods range from simple to complex optimization techniques. Majority of these methods generate adversaries through optimization objectives that are tied to the pre-softmax or softmax output of the network. In this work we, (i) show the drawbacks of such attacks, (ii) propose two new evaluation metrics: Old Label New Rank (OLNR) and New Label Old Rank (NLOR) in order to quantify the extent of damage made by an attack, and (iii) propose a new adversarial attack FDA: Feature Disruptive Attack, to address the drawbacks of existing attacks. FDA works by generating image perturbation that disrupt features at each layer of the network and causes deep-features to be highly corrupt. This allows FDA adversaries to severely reduce the performance of deep networks. We experimentally validate that FDA generates stronger adversaries than other state-of-the-art methods for image classification, even in the presence of various defense measures. More importantly, we show that FDA disrupts feature-representation based tasks even without access to the task-specific network or methodology. Code available at: https://github.com/BardOfCodes/fda, Comment: Accepted in ICCV;19. Code Available at https://github.com/BardOfCodes/fda
- Published
- 2019
25. Controlled Growth of Large-Area Bilayer Tungsten Diselenides with Lateral P-N Junctions
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Mandyam, Srinivas V., Zhao, Meng Qiang, Das, Paul Masih, Zhang, Qicheng, Price, Christopher C., Gao, Zhaoli, Shenoy, Vivek B., Drndic, Marija, and Johnson, Alan T. Charlie
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Condensed Matter - Materials Science - Abstract
Bilayer two-dimensional (2D) van der Waals (vdW) materials are attracting increasing attention due to their predicted high quality electronic and optical properties. Here we demonstrate dense, selective growth of WSe2 bilayer flakes by chemical vapor deposition with the use of a 1:10 molar mixture of sodium cholate and sodium chloride as the growth promoter to control the local diffusion of W-containing species. A large fraction of the bilayer WSe2 flakes showed a 0 and 60o twist between the two layers, while moire 15 and 30o-twist angles were also observed. Well-defined monolayer-bilayer junctions were formed in the as-grown bilayer WSe2 flakes, and these interfaces exhibited p-n diode rectification and an ambipolar transport characteristic. This work provides an efficient method for the layer-controlled growth of 2D materials, in particular, 2D transition metal dichalcogenides and promotes their applications in next-generation electronic and optoelectronic devices.
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- 2019
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26. Collagen microarchitecture mechanically controls myofibroblast differentiation
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Seo, Bo Ri, Chen, Xingyu, Ling, Lu, Song, Young Hye, Shimpi, Adrian A, Choi, Siyoung, Gonzalez, Jacqueline, Sapudom, Jiranuwat, Wang, Karin, Eguiluz, Roberto Carlos Andresen, Gourdon, Delphine, Shenoy, Vivek B, and Fischbach, Claudia
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Stem Cell Research ,Regenerative Medicine ,Bioengineering ,Stem Cell Research - Nonembryonic - Human ,Adipose Tissue ,Biomechanical Phenomena ,Cell Differentiation ,Cells ,Cultured ,Collagen ,Extracellular Matrix ,Fibronectins ,Humans ,Mechanotransduction ,Cellular ,Myofibroblasts ,Stromal Cells ,3D fibrous matrix mechanics ,adipose-derived stem cells ,collagen microarchitecture ,mechanosignaling ,myofibroblast differentiation - Abstract
Altered microarchitecture of collagen type I is a hallmark of wound healing and cancer that is commonly attributed to myofibroblasts. However, it remains unknown which effect collagen microarchitecture has on myofibroblast differentiation. Here, we combined experimental and computational approaches to investigate the hypothesis that the microarchitecture of fibrillar collagen networks mechanically regulates myofibroblast differentiation of adipose stromal cells (ASCs) independent of bulk stiffness. Collagen gels with controlled fiber thickness and pore size were microfabricated by adjusting the gelation temperature while keeping their concentration constant. Rheological characterization and simulation data indicated that networks with thicker fibers and larger pores exhibited increased strain-stiffening relative to networks with thinner fibers and smaller pores. Accordingly, ASCs cultured in scaffolds with thicker fibers were more contractile, expressed myofibroblast markers, and deposited more extended fibronectin fibers. Consistent with elevated myofibroblast differentiation, ASCs in scaffolds with thicker fibers exhibited a more proangiogenic phenotype that promoted endothelial sprouting in a contractility-dependent manner. Our findings suggest that changes of collagen microarchitecture regulate myofibroblast differentiation and fibrosis independent of collagen quantity and bulk stiffness by locally modulating cellular mechanosignaling. These findings have implications for regenerative medicine and anticancer treatments.
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- 2020
27. Distinguishing electronic contributions of surface and sub-surface transition metal atoms in Ti-based MXenes
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Yang, Yizhou, Hantanasirisakul, Kanit, Frey, Nathan C, Anasori, Babak, Green, Robert J, Rogge, Paul C, Waluyo, Iradwikanari, Hunt, Adrian, Shafer, Padraic, Arenholz, Elke, Shenoy, Vivek B, Gogotsi, Yury, and May, Steven J
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Physical Sciences ,Condensed Matter Physics ,Affordable and Clean Energy ,Macromolecular and Materials Chemistry ,Materials Engineering ,Nanotechnology ,Materials engineering ,Condensed matter physics - Abstract
MXenes are a rapidly-expanding family of 2D transition metal carbides and nitrides that have attracted attention due to their excellent performance in applications ranging from energy storage to electromagnetic interference shielding. Numerous other electronic and magnetic properties have been computationally predicted, but not yet realized due to the experimental difficulty in obtaining uniform surface terminations (Tx), necessitating new design approaches for MXenes that are independent of surface terminations. In this study, we distinguished the contributions of surface and sub-surface Ti atoms to the electronic structure of four Ti-containing MXenes (Ti2CTx, Ti3C2Tx, Cr2TiC2Tx, and Mo2TiC2Tx) using soft x-ray absorption spectroscopy. For MXenes with no Ti atoms on the surface transition metal layers, such as Mo2TiC2Tx and Cr2TiC2Tx, our results show minimal changes in the spectral features between the parent MAX phase and its MXene. In contrast, for MXenes with surface Ti atoms, here Ti3C2Tx and Ti2CTx, the Ti L-edge spectra are significantly modified compared to their parent MAX phase compounds. First principles calculations provide similar trends in the partial density of states derived from surface and sub-surface Ti atoms, corroborating the spectroscopic measurements. These results reveal that electronic states derived from sub-surface M-site layers are largely unperturbed by the surface terminations, indicating a relatively short length scale over which the Tx terminations alter the nominal electron count associated with Ti atoms and suggesting that desired band features should be hosted by sub-surface M-sites that are electronically more robust than their surface M-site counterparts.
- Published
- 2020
28. A narrative review of vaccine-induced thrombotic thrombocytopenia in organ donation and transplantation: Current evidence and implications
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Vivek B Kute, Sanshriti Chauhan, Narayan Prasad, and Hari Shankar Meshram
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deceased donation ,disseminated intravascular coagulation ,organ transplantation ,preimplantation biopsy ,severe acute respiratory syndrome coronavirus 2 vaccine ,vaccine-induced thrombotic thrombocytopenia ,Surgery ,RD1-811 - Abstract
Vaccine-induced thrombotic thrombocytopenia (VITT) has been recently linked with coronavirus disease (COVID-19) vaccines. It becomes crucial for the transplant communities to have a rigorous approach for accepting VITT donors, as the reports of such transplantation have been associated with thrombotic complications, graft loss, and deaths. The magnitude of facing a VITT donor in transplantation practices is unknown and also the management protocol. However, as per the limited data, it is better to avoid such transplants, and in the case of emergency transplants, the risk-benefit ratio should be weighed. All transplantation from VITT donors should be appropriately counseled before procurement. The organs should undergo deliberate examination for functionality by clinical, laboratory, and radiological parameters. In doubtful cases, a preimplantation biopsy is mandated to rule out any thrombosis. VITT donors are suggested to be treated with newer oral anti-coagulation and intravenous immunoglobulin. Platelet transfusion is best avoided in a VITT donor. There is no established protocol for any modification in surgical procedure, anesthesia, or immunosuppressive medicines in the recipients. The recipients should undergo extensive clinical and laboratory monitoring for any possible complications. No prophylactic therapy is recommended at present but candidates with a history of any COVID-19 vaccine within 30 days, should be avoided. In summary, the evidence for diagnosis and management of VITT donors is based only on a few reports, but with current knowledge, it is advisable to take a multidisciplinary approach to assess all benefits and risks before accepting or discarding organs.
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- 2023
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29. Thermal insulation panels for buildings using recycled cardboard: Experimental characterization and optimum selection
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Mathews, Jemi Merrin, Vivek, B., and Charde, Meghana
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- 2023
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30. Feedback between mechanosensitive signaling and active forces governs endothelial junction integrity
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Eoin McEvoy, Tal Sneh, Emad Moeendarbary, Yousef Javanmardi, Nadia Efimova, Changsong Yang, Gloria E. Marino-Bravante, Xingyu Chen, Jorge Escribano, Fabian Spill, José Manuel Garcia-Aznar, Ashani T. Weeraratna, Tatyana M. Svitkina, Roger D. Kamm, and Vivek B. Shenoy
- Subjects
Science - Abstract
Gap formation in the vasculature underpins immune and tumour cell infiltration. Here the authors propose a chemo-mechanical model to analyse how feedback between mechanosensitive signalling, active cellular forces and adhesion governs the breakdown, recovery, and integrity of endothelial junctions.
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- 2022
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31. Gray-box Adversarial Training
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S., Vivek B., Mopuri, Konda Reddy, and Babu, R. Venkatesh
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Computer Science - Computer Vision and Pattern Recognition ,Computer Science - Machine Learning ,Statistics - Machine Learning - Abstract
Adversarial samples are perturbed inputs crafted to mislead the machine learning systems. A training mechanism, called adversarial training, which presents adversarial samples along with clean samples has been introduced to learn robust models. In order to scale adversarial training for large datasets, these perturbations can only be crafted using fast and simple methods (e.g., gradient ascent). However, it is shown that adversarial training converges to a degenerate minimum, where the model appears to be robust by generating weaker adversaries. As a result, the models are vulnerable to simple black-box attacks. In this paper we, (i) demonstrate the shortcomings of existing evaluation policy, (ii) introduce novel variants of white-box and black-box attacks, dubbed gray-box adversarial attacks" based on which we propose novel evaluation method to assess the robustness of the learned models, and (iii) propose a novel variant of adversarial training, named Graybox Adversarial Training" that uses intermediate versions of the models to seed the adversaries. Experimental evaluation demonstrates that the models trained using our method exhibit better robustness compared to both undefended and adversarially trained model, Comment: Accepted to ECCV 2018
- Published
- 2018
32. Rigidity controls human desmoplastic matrix anisotropy to enable pancreatic cancer invasion via extracellular signal-regulated kinase 2
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Malik, Ruchi, Luong, Tiffany, Cao, Xuan, Han, Biao, Shah, Neelima, Han, Lin, Shenoy, Vivek B., Lelkes, Peter I., and Cukierman, Edna
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Quantitative Biology - Cell Behavior - Abstract
Only about 8 percent of patients with pancreatic ductal adenocarcinoma, PDAC, live up to 5 years following diagnosis; by 2020 PDAC will become the second most lethal cancer in the United States. PDAC includes an anisotropic fibrous-like stroma, desmoplasia, encompassing most of the tumor mass. Desmoplasia is produced by cancer-associated fibroblasts, CAFs, and their cell-derived extracellular matrices, CDMs. Since elimination of CAFs is detrimental to patients, CDM reprogramming, as opposed to desmoplasia ablation, is therapeutically desirable. In this study we used a human mimetic three-dimensional CAF producing CDM system and proceeded to study its dynamic architectural modifications, following underlying substrate stiffness alterations, using digital imaging analyses, atomic force microscopy, mathematical modeling, cell biology, biochemistry and human tissue quantitative simultaneous multiplex immunofluorescence. Results suggested that the architecture of CDMs can be manipulated to render a tumor-suppressive microenvironment. We posit that perhaps treatments that could reprogram desmoplasia to become tumor-restrictive or that could target tumoral ERK2 might provide future new means for treating PDAC patients., Comment: Main text with 6 figures, 1 table and references, including 5 supplemental figures and legends as well as one supplemental table and a movie legend with corresponding link
- Published
- 2018
33. Task-based Parallel Computation of the Density Matrix in Quantum-based Molecular Dynamics using Graph Partitioning
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Ghale, Purnima, Kroonblawd, Matthew P., Mniszewski, Susan M., Negre, Christian F. A., Pavel, Robert, Pino, Sergio, Sardeshmukh, Vivek B., Shi, Guangjie, and Hahn, Georg
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Physics - Computational Physics ,Quantum Physics - Abstract
Quantum-based molecular dynamics (QMD) is a highly accurate and transferable method for material science simulations. However, the time scales and system sizes accessible to QMD are typically limited to picoseconds and a few hundred atoms. These constraints arise due to expensive self-consistent ground-state electronic structure calculations that can often scale cubically with the number of atoms. Linearly scaling methods depend on computing the density matrix P from the Hamiltonian matrix H by exploiting the sparsity in both matrices. The second-order spectral projection (SP2) algorithm is an O(N) algorithm that computes P with a sequence of 40-50 matrix-matrix multiplications. In this paper, we present task-based implementations of a recently developed data-parallel graph-based approach to the SP2 algorithm, G-SP2. We represent the density matrix P as an undirected graph and use graph partitioning techniques to divide the computation into smaller independent tasks. The partitions thus obtained are generally not of equal size and give rise to undesirable load imbalances in standard MPI-based implementations. This load-balancing challenge can be mitigated by dynamically scheduling parallel computations at runtime using task-based programming models. We develop task-based implementations of the data-parallel G-SP2 algorithm using both Intel's Concurrent Collections (CnC) as well as the Charm++ programming model and evaluate these implementations for future use. Scaling and performance results of our implementations are investigated for representative segments of QMD simulations for solvated protein systems containing more than 10,000 atoms.
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- 2018
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34. Modeling links softening of myelin and spectrin scaffolds of axons after a concussion to increased vulnerability to repeated injuries
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Kant, Aayush, Johnson, Victoria E., Arena, John D., Dollé, Jean-Pierre, Smith, Douglas H., and Shenoy, Vivek B.
- Published
- 2021
35. Efficient microwave absorption with Vn+1CnTx MXenes
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Han, Meikang, Shuck, Christopher E., Singh, Akash, Yang, Yizhou, Foucher, Alexandre C., Goad, Adam, McBride, Bernard, May, Steven J., Shenoy, Vivek B., Stach, Eric A., and Gogotsi, Yury
- Published
- 2022
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36. Genetic trends in CIMMYT’s tropical maize breeding pipelines
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Prasanna, Boddupalli M., Burgueño, Juan, Beyene, Yoseph, Makumbi, Dan, Asea, Godfrey, Woyengo, Vincent, Tarekegne, Amsal, Magorokosho, Cosmos, Wegary, Dagne, Ndhlela, Thokozile, Zaman-Allah, Mainassara, Matova, Prince M., Mwansa, Kabamba, Mashingaidze, Kingstone, Fato, Pedro, Teklewold, Adefris, Vivek, B. S., Zaidi, P. H., Vinayan, M. T., Patne, Nagesh, Rakshit, Sujay, Kumar, Ramesh, Jat, S. L., Singh, S. B., Kuchanur, Prakash H., Lohithaswa, H. C., Singh, N. K., Koirala, K. B., Ahmed, Salahuddin, Vicente, Felix San, Dhliwayo, Thanda, and Cairns, Jill E.
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- 2022
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37. Feedback between mechanosensitive signaling and active forces governs endothelial junction integrity
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McEvoy, Eoin, Sneh, Tal, Moeendarbary, Emad, Javanmardi, Yousef, Efimova, Nadia, Yang, Changsong, Marino-Bravante, Gloria E., Chen, Xingyu, Escribano, Jorge, Spill, Fabian, Garcia-Aznar, José Manuel, Weeraratna, Ashani T., Svitkina, Tatyana M., Kamm, Roger D., and Shenoy, Vivek B.
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- 2022
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38. Management strategies and outcomes in renal transplant recipients recovering from COVID-19: A retrospective, multicentre, cohort study
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Kute, Vivek B., Ray, Deepak S., Aziz, Feroz, Godara, Suraj M., Hegde, Umapati, KumarBT, Anil, Bhalla, Anil K., Yadav, Dinesh Kumar, Singh, Sarbpreet, Pathak, Vivek, Dalal, Sonal, Bahadur, Madan M., Anandh, Urmila, Abraham M, Abi, Siddini, Vishwanath, Das, Sushree Sashmita, Thukral, Sharmila, Krishnakumar, Arvind, Sharma, Ashish, Kher, Vijay, Bansal, Shyam B., Shingare, Ashay, Narayanan, Ranjit, Patel, Himanshu, Gulati, Sanjeev, Kakde, Shailesh, Bansal, Dinesh, Guleria, Sandeep, Khullar, Dinesh, Gumber, Manoj R., Varyani, Umesh, Guditi, Swarnalatha, Khetan, Prakash, Dave, Rutul, Mishra, Vineet V., Tullius, Stefan G., Chauhan, Sanshriti, and Meshram, Hari Shankar
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- 2022
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39. Janus Monolayer Transition Metal Dichalcogenides
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Zhang, Jing, Jia, Shuai, Iskandar, Kholmanov, Dong, Liang, Er, Dequan, Chen, Weibing, Guo, Hua, Jin, Zehua, Shenoy, Vivek B., Shi, Li, and Lou, Jun
- Subjects
Condensed Matter - Materials Science - Abstract
A novel crystal configuration of sandwiched S-Mo-Se structure (Janus SMoSe) at the monolayer limit has been synthesized and carefully characterized in this work. By controlled sulfurization of monolayer MoSe2 the top layer of selenium atoms are substituted by sulfur atoms while the bottom selenium layer remains intact. The peculiar structure of this new material is systematically investigated by Raman, photoluminescence and X-ray photoelectron spectroscopy and confirmed by transmission-electron microscopy and time-of-flight secondary ion mass spectrometry. Density-functional theory calculations are performed to better understand the Raman vibration modes and electronic structures of the Janus SMoSe monolayer, which are found to correlate well with corresponding experimental results. Finally, high basal plane hydrogen evolution reaction (HER) activity is discovered for the Janus monolayer and DFT calculation implies that the activity originates from the synergistic effect of the intrinsic defects and structural strain inherent in the Janus structure., Comment: 22 pages, 12 figures
- Published
- 2017
40. Comparative Analysis of Kidney Transplant Recipients with Severe Acute Respiratory Syndrome Coronavirus 2 Compared with Nonkidney Transplant Recipients: A Largest Single-center Report from the Second Wave of Coronavirus Disease 2019 Pandemic in South East Asia
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Sanshriti Chauhan, Hari Shankar Meshram, Vivek B Kute, Himanshu Patel, Sandeep Deshmukh, Sudeep Desai, Ruchir Dave, and Subho Banerjee
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Medicine - Abstract
Outcomes of severe acute respiratory syndrome coronavirus 2 in kidney transplant recipients (KTR) compared with matched cohort are certainly lacking for different pandemic waves and geographic regions. In this single-center retrospective study of coronavirus disease-2019 (COVID-19) cases admitted during March 26, 2021 to June 7, 2021, a propensity-matched analysis in a 1:1 ratio was performed to compare the clinical profile and outcomes between KTR and non-KTR. A Cox proportional hazard model from the whole study population to analyze risk factors for severe disease and mortality was calculated. We identified 1052 COVID-19 cases, of which 107 (10.1%) were KTR. In propensity-matched analysis, KTR had higher fever (81.6 % vs. 60%; P = 0.01), lymphopenia (30% vs. 11.7%; P = 0.02), higher neutrophil-to-lymphocyte ratio (43.3% vs. 25%; P = 0.05), and acute kidney injury (66.6% vs. 36.7%; P = 0.001). In Kaplan–Meier survival analysis, there was no difference in mortality or severity of COVID-19. In Cox hazard proportional analysis, the European cooperative oncology group (ECOG) score of 1 to 2 [Hazard ratio (HR) 95% lower confidence interval (CI), upper CI = 4.9 (1.8–13.5); P 2 [HR = 20 (7.5, 54.7); P
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- 2022
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41. Role of telemedicine in kidney transplant recipient in COVID 19 era
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Vivek B Kute, Vaibhav Gupta, Himanshu V Patel, Subho Banerjee, Divyesh P Engineer, Harishankar Meshram, Vijay Navadia, and Ansy H Patel
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coronavirus ,covid-19 ,kidney transplant recipients ,telehealth ,telemedicine ,Surgery ,RD1-811 - Abstract
Introduction: Telemedicine represents an innovative but untested approach to maintain patient care and reduce the risk of COVID-19 exposure to patients, health-care workers, and the public. In this study, we evaluated the applicability and efficacy of telemedicine in a kidney transplant recipient (KTR) cohort in COVID 19 era. Materials and Methods: An observational cohort study was conducted at a tertiary-care public-sector kidney disease institute in western India between March and September 2020. We evaluated the reasons, modes, and outcomes of patient contacts by telemedicine in the KTR cohort. We also evaluated the utility of telemedicine across three age groups. Results: Of 840 participants, whose mean age was 38.78 ± 12.39 years, male to female ratio was 4:1. The most common mode of communication was WhatsApp (653, 77.7%) followed by in-person surrogates (126, 15%). Acceptability of telemedicine was significantly better in younger and middle-age groups (P < 0.00001) compared to the elderly. Request for drug delivery (n = 756) was the most common reason for contact overall and managed through postal parcels. KTRs (n = 200) and donors (n = 75) were evaluated for medical illnesses. The most common medical reasons for contact were for febrile illness (n = 120) and graft dysfunction (n = 60). COVID-19-related disease was diagnosed and managed in 80 KTRs and 2 donors. COVID-19 updates were given to all contacts. Conclusion: Telemedicine is underutilized in the care of the KTR cohort. Telemedicine can be used across all ages although it's best suited for young and middle age groups. The impact of telemedicine on short- and long-term patient outcomes is unclear and warrants further study.
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- 2022
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42. On the way to mandate booster vaccine dose of coronavirus disease 2019 for transplant recipients: A narrative review of literature
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Vivek B Kute, Sudeep Nimish Desai, Hari Shankar Meshram, Kinjal Narendra Shah, Sanshriti Chauhan, Vineet V Mishra, and Manisha Sahay
- Subjects
booster dose ,coronavirus disease 2019 vaccine ,solid organ transplant ,Surgery ,RD1-811 - Abstract
Coronavirus disease 2019 (COVID-19) vaccine efficacy, especially against severe disease is known to wane over time. We examined current knowledge of COVID-19 vaccine booster dose in solid organ transplant recipients (SOTR). We have systematically searched PubMed, EMBASE, MEDLINE, Scopus and Google Scholar with the following MeSH terms: “SARS-CoV-2 vaccine,” or “COVID-19 vaccine,” and “organ transplantation” and “booster” or “third dose.” This review article examines a number of studies including guidelines from professional societies examining the safety as well as increased immunogenicity of a booster dose among SOTR. Equitable distribution of vaccines across the globe is the need of the hour. While some countries are well into the booster dose phase, the lower-income countries are languishing behind with primary doses for their health workers. Available reports suggest less efficacy of COVID-19 vaccine in SOTR suggesting booster dose for them. Several studies highlighted the safety and efficacy of COVID-19 vaccines booster dose among SOTR. SOTR should also continue to adhere to all safety and COVID-19 appropriate behaviors. There is a growing need for alternative strategies to improve protection. As Omicron cases rise around the world, India announced that COVID-19 vaccination for children aged 15–18 years and “precautionary (booster) doses” would be administered to healthcare and frontline workers and people above 60 years of age with comorbidities from January 2022. In near future, with increased availability of vaccinations, all SOTR will have access to booster dose in a phased manner.
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- 2022
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43. NOTTO guidelines for vaccine-induced thrombotic thrombocytopenia in organ donation and transplantation
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Vivek B Kute, Sonal Asthana, Subhash Gupta, Sanjay K Agarwal, Swarnalatha Guditi, Manisha Sahay, Sujoy Pal, S Sudhindran, Ashish Sharma, Sandeep Seth, Alla Gopala Krishna Gokhale, Milind Dhahir Hote, Arpita Ray Chaudhury, Arvinder Singh Soin, Mohamed Rela, Rajesh Malhotra, Virinder K Bansal, Devinder Singh Rana, Rajneesh Sahai, and Vasanthi Ramesh
- Subjects
covid-19 ,deceased donor ,national organ and tissue transplant organization ,organ donation ,transplantation ,vaccine-induced thrombotic thrombocytopenia ,Surgery ,RD1-811 - Abstract
From the context of organ donation, COVID-19 vaccine-induced thrombotic thrombocytopenia (VITT) is important as there is an ethical dilemma in utilizing versus discarding organs from potential donors succumbing to VITT. This consensus statement is an attempt by the National Organ and Tissue Transplant Organization (NOTTO) apex technical committees, India, to formulate the guidelines for deceased organ donation and transplantation in relation to VITT to help in appropriate decision-making. VITT is a rare entity, but a meticulous approach should be taken by the organ procurement organization's (OPO) team in screening such cases. All such cases must be strictly notified to the national authorities (NOTTO) as a resource for data collection and ensuring compliance with protocols in the management of adverse events following immunization. Organs from any patient who developed thrombotic events up to 4 weeks after adenoviral vector-based vaccination should be considered to be linked to VITT and investigated appropriately. The viability of the organs must be thoroughly checked by the OPO, and the final decision in relation to organ use should be decided by the expert committee of the OPO team consisting of a virologist, a hematologist, and a treating team. Considering the organ shortage, in case of suspected/confirmed VITT, both clinicians and patients should consider the risk‒benefit equation based on limited experience. An appropriate written informed consent of potential recipients and family members should be obtained before the transplantation of organs from suspected or proven VITT donors.
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- 2022
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44. Clinical perspectives towards improving risk stratification strategy for renal transplantation outcomes in Indian patients
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Vijay Kher, Vivek B Kute, Sarbeswar Sahariah, Deepak S Ray, Dinesh Khullar, Sandeep Guleria, Shyam Bansal, Sishir Gang, Anil Kumar Bhalla, Jai Prakash, Abi Abraham, Sunil Shroff, Madan M Bahadur, Pratik Das, Urmila Anandh, Arpita Ray Chaudhury, Manoj Singhal, Jatin Kothari, Sree Bhushan Raju, Dilip Kumar Pahari, G Vishwanath Siddini, G Sudhakar, Santosh Varughese, and Tarun K Saha
- Subjects
acute rejection ,donor-specific antibody ,human leukocyte antigens ,immunosuppression ,indian patients ,living donors ,renal transplantation ,Surgery ,RD1-811 - Abstract
Graft loss and rejections (acute/chronic) continue to remain important concerns in long-term outcomes in kidney transplant despite newer immunosuppressive regimens and increased use of induction agents. Global guidelines identify the risk factors and suggest a framework for management of patients at different risk levels for rejection; however, these are better applicable to deceased donor transplants. Their applicability in Indian scenario (predominantly live donor program) could be a matter of debate. Therefore, a panel of experts discussed the current clinical practice and adaptability of global recommendations to Indian settings. They also took a survey to define risk factors in kidney transplants and provide direction toward evidence- and clinical experience-based risk stratification for donor/recipient and transplant-related characteristics, with a focus on living donor transplantations. Several recipient related factors (dialysis, comorbidities, and age, donor-specific antibodies [DSAs]), donor-related factors (age, body mass index, type – living or deceased) and transplantation related factors (cold ischemia time [CIT], number of transplantations) were assessed. The experts suggested that immunological conflict should be avoided by performing cytotoxic cross match, flow cross match in all patients and DSA-(single antigen bead) whenever considered clinically relevant. HLA mismatches, presence of DSA, along with donor/recipient age, CIT, etc., were associated with increased risk of rejection. Furthermore, the panel agreed that the risk of rejection in living donor transplant is not dissimilar to deceased donor recipients. The experts also suggested that induction immunosuppression could be individualized based on the risk stratification.
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- 2022
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45. Mechanisms of Plastic Deformation in Collagen Networks Induced by Cellular Forces
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Ban, Ehsan, Franklin, J Matthew, Nam, Sungmin, Smith, Lucas R, Wang, Hailong, Wells, Rebecca G, Chaudhuri, Ovijit, Liphardt, Jan T, and Shenoy, Vivek B
- Subjects
Bioengineering ,Cancer ,Animals ,Biomechanical Phenomena ,Collagen ,Extracellular Matrix ,Fibroblasts ,Mechanical Phenomena ,Mice ,Models ,Biological ,NIH 3T3 Cells ,Rats ,Spheroids ,Cellular ,Stress ,Mechanical ,Physical Sciences ,Chemical Sciences ,Biological Sciences ,Biophysics - Abstract
Contractile cells can reorganize fibrous extracellular matrices and form dense tracts of fibers between neighboring cells. These tracts guide the development of tubular tissue structures and provide paths for the invasion of cancer cells. Here, we studied the mechanisms of the mechanical plasticity of collagen tracts formed by contractile premalignant acinar cells and fibroblasts. Using fluorescence microscopy and second harmonic generation, we quantified the collagen densification, fiber alignment, and strains that remain within the tracts after cellular forces are abolished. We explained these observations using a theoretical fiber network model that accounts for the stretch-dependent formation of weak cross-links between nearby fibers. We tested the predictions of our model using shear rheology experiments. Both our model and rheological experiments demonstrated that increasing collagen concentration leads to substantial increases in plasticity. We also considered the effect of permanent elongation of fibers on network plasticity and derived a phase diagram that classifies the dominant mechanisms of plasticity based on the rate and magnitude of deformation and the mechanical properties of individual fibers. Plasticity is caused by the formation of new cross-links if moderate strains are applied at small rates or due to permanent fiber elongation if large strains are applied over short periods. Finally, we developed a coarse-grained model for plastic deformation of collagen networks that can be employed to simulate multicellular interactions in processes such as morphogenesis, cancer invasion, and fibrosis.
- Published
- 2018
46. BK polyomavirus infection following COVID-19 infection in renal transplant recipients: a single-center experience
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Hari Shankar Meshram, Vivek B. Kute, and Sanshriti Chauhan
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Internal medicine ,RC31-1245 ,Specialties of internal medicine ,RC581-951 - Published
- 2021
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47. Super-fast MST Algorithms in the Congested Clique using $o(m)$ Messages
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Pemmaraju, Sriram V. and Sardeshmukh, Vivek B.
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Computer Science - Distributed, Parallel, and Cluster Computing - Abstract
In a sequence of recent results (PODC 2015 and PODC 2016), the running time of the fastest algorithm for the \emph{minimum spanning tree (MST)} problem in the \emph{Congested Clique} model was first improved to $O(\log \log \log n)$ from $O(\log \log n)$ (Hegeman et al., PODC 2015) and then to $O(\log^* n)$ (Ghaffari and Parter, PODC 2016). All of these algorithms use $\Theta(n^2)$ messages independent of the number of edges in the input graph. This paper positively answers a question raised in Hegeman et al., and presents the first "super-fast" MST algorithm with $o(m)$ message complexity for input graphs with $m$ edges. Specifically, we present an algorithm running in $O(\log^* n)$ rounds, with message complexity $\tilde{O}(\sqrt{m \cdot n})$ and then build on this algorithm to derive a family of algorithms, containing for any $\varepsilon$, $0 < \varepsilon \le 1$, an algorithm running in $O(\log^* n/\varepsilon)$ rounds, using $\tilde{O}(n^{1 + \varepsilon}/\varepsilon)$ messages. Setting $\varepsilon = \log\log n/\log n$ leads to the first sub-logarithmic round Congested Clique MST algorithm that uses only $\tilde{O}(n)$ messages. Our primary tools in achieving these results are (i) a component-wise bound on the number of candidates for MST edges, extending the sampling lemma of Karger, Klein, and Tarjan (Karger, Klein, and Tarjan, JACM 1995) and (ii) $\Theta(\log n)$-wise-independent linear graph sketches (Cormode and Firmani, Dist.~Par.~Databases, 2014) for generating MST candidate edges., Comment: Full version of FST-TCS 2016 paper with the same title
- Published
- 2016
48. Graph Partitioning Methods for Fast Parallel Quantum Molecular Dynamics
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Djidjev, Hristo N., Hahn, Georg, Mniszewski, Susan M., Negre, Christian F. A., Niklasson, Anders M. N., and Sardeshmukh, Vivek B.
- Subjects
Quantum Physics - Abstract
We study a graph partitioning problem motivated by the simulation of the physical movement of multi-body systems on an atomistic level, where the forces are calculated from a quantum mechanical description of the electrons. Several advanced algorithms have been published in the literature for such simulations that are based on evaluations of matrix polynomials. We aim at efficiently parallelizing these computations by using a special type of graph partitioning. For this, we represent the zero-nonzero structure of a thresholded matrix as a graph and partition that graph into several components. The matrix polynomial is then evaluated for each separate submatrix corresponding to the subgraphs and the evaluated submatrix polynomials are used to assemble the final result for the full matrix polynomial. The paper provides a rigorous definition as well as a mathematical justification of this partitioning problem. We use several algorithms to compute graph partitions and experimentally evaluate their performance with respect to the quality of the partition obtained with each method and the time needed to produce it.
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- 2016
49. Assessment of Healthcare Resource Utilization by Anticoagulant Heparinoid Dosage Level in Patients Hospitalized with COVID-19
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Keith Robinson MD, Laura L. Schott PhD, Tom Matthews MPH, Manu Tyagi MBA, Vivek B. Ajmani PhD, Nancy Sacco PhD, and Zhun Cao PhD
- Subjects
Diseases of the circulatory (Cardiovascular) system ,RC666-701 - Abstract
The aim was to describe inpatients with COVID-19 empirically prescribed heparinoid anticoagulants and compare resource utilization between prophylactic/low-dose and therapeutic/high-dose groups. Methods: This retrospective observational study used real-world data from 880 US hospitals in the PINC AI™ Healthcare Database during 4/1/2020–11/30/2020. Descriptive analysis was used to characterize patients. Multivariable regression was used to evaluate intensive care unit (ICU) admissions, length of stay (LOS), mortality, and costs by anticoagulation dose group, adjusting for cohort characteristics. Among 122,508 inpatients, 29,225 (23.9%) received therapeutic/high-dose, and 93,283 (76.1%) received prophylactic/low-dose anticoagulation. The high-dose group had more comorbidities and worse laboratory values compared with low-dose. Respectively, ICU admission rates were 36.7% and 19.1% and LOS median (Q1, Q3) was 8 (5, 15) and 5 (3, 9) days. In separate adjusted models, high-dose anticoagulation was associated with a 45% increase in odds of ICU admission, 26% increase in odds of in-hospital mortality, 21% longer average LOS, and 28% greater average total cost compared with low-dose (each P
- Published
- 2022
- Full Text
- View/download PDF
50. Soft robotic constrictor for in vitro modeling of dynamic tissue compression
- Author
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Jungwook Paek, Joseph W. Song, Ehsan Ban, Yuma Morimitsu, Chinedum O. Osuji, Vivek B. Shenoy, and Dan Dongeun Huh
- Subjects
Medicine ,Science - Abstract
Abstract Here we present a microengineered soft-robotic in vitro platform developed by integrating a pneumatically regulated novel elastomeric actuator with primary culture of human cells. This system is capable of generating dynamic bending motion akin to the constriction of tubular organs that can exert controlled compressive forces on cultured living cells. Using this platform, we demonstrate cyclic compression of primary human endothelial cells, fibroblasts, and smooth muscle cells to show physiological changes in their morphology due to applied forces. Moreover, we present mechanically actuatable organotypic models to examine the effects of compressive forces on three-dimensional multicellular constructs designed to emulate complex tissues such as solid tumors and vascular networks. Our work provides a preliminary demonstration of how soft-robotics technology can be leveraged for in vitro modeling of complex physiological tissue microenvironment, and may enable the development of new research tools for mechanobiology and related areas.
- Published
- 2021
- Full Text
- View/download PDF
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